LYSIS 7.1 for Windows (9x/NT/2000/XP)
A Comprehensive Package for Time Series Data Analysis
&
Linear/Nonlinear System Modeling and Simulatio
Updates: 1997, 2001, 2005, 2009
Developed under the sponsorship from the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health and funded by Grant P41-EB001978.
Biomedical Simulations Resource University of Southern California 1042 Downey Way, DRB 367 Los Angeles, CA 90089-1111 Telephone (213) 740-0342 Fax (213) 740-0343 Email: [email protected]
CONTENTS
LYSIS 7.1 for Windows (9x/NT/2000/XP) is distributed as a compressed (ZIP) via the BMSR Website. The distribution medium contains LYSIS 7.1 executable files, the required installation files and documentation files (README.TXT and LYSIS7.PDF). The file README.TXT provides basic instructions and the file LYSIS7.PDF provides the list of programs included in LYSIS 7.1 with a brief description of the function of each program. A tutorial is also included (documents TUTOR1.PDF and TUTOR2.PDF) that introduces LYSIS 7.1 to the user with illustrative examples.
BRIEF DESCRIPTION
LYSIS is a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include nonlinear input-output modeling for biomedical applications.
LYSIS 7.1 is available to download from the BMSR website in a form that can run on Windows (9x/NT/2000/XP). It is also available for UNIX environments in the form of source code to be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux, etc).
The Windows 9x and WinNT versions of LYSIS 7.1 come bundled with the PGPLOT library and fonts (PGPLOT.LIB,GRFONT.DAT, and RGB.TXT), which are necessary for the graphics programs to operate, when installed in the same folder as LYSIS 7.1.
LYSIS 7.1 is packed with the required files to make all necessary modifications to the Windows 9x/NT environment, with only minimal changes in environment (adjusting a few variables). The installation creates the LYSIS 7.1 Group (and ten subgroups) upon pressing the Start button. Uninstalling LYSIS 7.1 can be accomplished through Control Panel - Add/Remove programs.
COMPUTER REQUIREMENTS (Intel Based Machines)
Minimum system requirements to run LYSIS 7.1 are:
- Intel P5 (or better) based computer
- 256 Mbytes of RAM or more
- MS-Windows 95/98 or NT v4 with SP3
- disk space of at least 35 Mbytes
- 1GB pagefile
- video card capable of 256 colors or better
INSTALLATION OVERVIEW
Installation of LYSIS 7.1 takes place in four steps:
(1) Decompress LYSIS files into a temporary directory. Then go to the directory you decompressed the files and run SETUP.EXE to start the installation process. (2) Once the installation process has begun, the program will first search for previous installations of LYSIS and will prompt you to continue the installation. (3) Read and approve the license agreement that is presented to you during the installation. You will be presented with the option of changing the default directory to install LYSIS 7.1 and once you have selected the folder to install LYSIS 7.1, the installation program will continue to copy the program files into the selected directory. (4) Once the files have been copied onto the hard drive, you will be presented with the option of allowing the installation program to add the appropriate environment variables to your AUTOEXEC.BAT (Windows 9x users) or to the internal environment table (WinNT users). The environment variables required by LYSIS 7.1 are:
SET PGPLOT_FONT=C:\LYSIS71\GRFONT.DAT
SET PGPLOT_RGB=C:\LYSIS71\RGB.TXT
SET PGPLOT_BACKGROUND=WHITE
SET PGPLOT_FOREGROUND=BLACK
Adjust "C:\LYSIS71" accordingly to the directory where LYSIS 7.1 is installed. The foreground and background colors can be changed to your preference.
If you elected to make the necessary modifications to your AUTOEXEC.BAT file (Windows 9x users) then a backup copy of your AUTOEXEC.BAT file will be saved to AUTOEXEC.LYS in the root directory.
NOTE: Un-installation of LYSIS 7.1 will NOT remove the environment variables that have been set. The user is responsible for removing those entries, so that the removal does not affect other programs that may require them for proper operation.
At this point installation is complete.
After setting the appropriate variables in the AUTOEXEC.BAT file, reboot your machine if a Windows 9x users. Windows NT users may not require a reboot.
LIST OF HELPFUL HINTS
This is a list of helpful hints to assist the user with installation and maintenance of LYSIS 7.1.
1. Graphs from the plotting programs can be printed or incorporated into a document or worksheet using the clipboard.
2. To print the postscript file generated by the plotting programs, you need a postscript printer.
3. A comprehensive description of the Program Groups and the Programs file can be found in LYSIS7.PDF that is included in this package.
4. If you are running at a color depth of 32-bits, you may have problems running some of the Windows based modules (i.e. PLOT.EXE, etc.). If this is the case then try reducing your display color depth to 16-bits.
5. For LYSIS 7.1 installations on Windows NT that use Internet Browser or Communicator as the default (and only) browser, to open the html LYSIS page in order to obtain access to LYSIS programs, you must do the following:
In every session, when you access the first LYSIS file, the browser will prompt you to respond whether you want to open that file or not. Choose "Open it" and make sure that the box next to "Always ask before opening this file" is UNCHECKED. This will enable you to run the rest of the LYSIS files without being asked again.
TUTORIALS
Two tutorial sessions (TUTOR1.PDF and TUTOR2.PDF) are also included. They are PDF documents introducing the user to the various LYSIS program modules via two examples: one on Kernel Estimation and Non-Parametric Modeling and the other on Parametric Modeling.
LYSIS DATA FILE FORMAT
LYSIS produces and reads ASCII (text) files in the form of 1-D or 2-D datasets.
1-D datasets have a Header (bold) followed by a vector-list of the data-points in the format:
<1st-data-point> var-type-real
<2nd-data-point> var-type-real
etc.
2-D datasets have the following format with a Header (bold) and the data-points listed in the form of successive column vectors separated by blank lines:
<1st-data-point of 1st column vector> var-type-real
<2nd-data-point of 1st column vector > var-type-real
.
.
.
<1st-data-point of 2nd column vector> var-type-real
<2nd-data-point of 2nd column vector> var-type-real
.
.
.
<1st-data-point of 3rd column vector> var-type-real etc.